It isn't so much the subject but what it was tied to, the song of the French Revolution. The French government adopted the La Marsaillaise within a year of its creation as it's anthem and tried to use it for patriotic encouragement but for Napoleon, it's something else, it's a reminder of the Revolution.

Now, Napoleon want entirely against the Revolution. I've argued frequently that Napoleon didn't end the Revolution but moderated it and he may have seen himself as such, but as a leader he wanted to ensure that his France would be the one that would last, and by allowing the anthem of the Revolution continue during his rule would be disruptive to the national narriative.

However, during the dark days of 1814, he started to allow bands to start playing it in hopes of inspiring national fervor against the Allied horde.